FALL-RUN CHINOOK SALMON SPAWNER ESCAPEMENT SURVEY MAINSTEM ... chinook salmon spawner escapement survey ... fall-run chinook salmon spawner escapement survey mainstem sacramento ... through a fish ladder

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    Stream Flow and Habitat Evaluation Program


    MAINSTEM SACRAMENTO RIVEROctober - December 1995

    Prepared by

    Bill SniderBob Reavis

    andLarry Hanson

    Stream Evaluation ProgramTechnical Report No. 96-6

    October 1996


    Stream Flow and Habitat Evaluation Program


    MAINSTEM SACRAMENTO RIVEROctober - December 19951/,2/

    Prepared by

    Bill SniderBob Reavis

    andLarry Hanson

    October 1996

    1/ This work was supported by funds provided by the U.S. Fish and Wildlife Service, CentralValley Anadromous Fish Restoration Program, as part of a cooperative agreement with theCalifornia Department of Fish and Game pursuant to the Central Valley Project Improvement Act(PL. 102-575).

    2/ Stream Evaluation Program Technical Report 96-6.

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    The California Department of Fish and Games (DFG) Stream Flow and Habitat EvaluationProgram (SF&HEP) conducted an intensive fall-run chinook salmon escapement survey on themainstem Sacramento River during the fall-winter of 1995 to estimate fall-run chinook salmonspawner abundance and distribution. This survey was carried out to accommodate the mandatesof Section 3406(b)(1)(B) of the Central Valley Project Improvement Act (CVPIA), P.L. 102-575,that requires the Secretary of the Interior to determine instream flow needs for all Central ValleyProject controlled streams and rivers. Flow-need recommendations are to be provided to theSecretary by the U. S. Fish and Wildlife Service (FWS) after consultation with DFG. In responseto this Act, the FWS and the DFG entered a Cooperative Agreement to determine flow needsof anadromous salmonids in the mainstem Sacramento River.

    The primary mission of the SF&HEP - to improve understanding of the relationships betweensalmon and habitat in the mainstem Sacramento River - requires reliable estimates of the spawnerpopulation to help distinguish habitat versus population influences on temporal and spatialspawning distribution (Snider and McEwan 1992, Snider et al. 1993, and Snider and Vyverberg1995). Changes in spawning activity related to changes in flow and temperature need to bedistinguished from changes due to population size. Spawning density, redd superimposition,habitat use, and other parameters can be affected by both changes in habitat conditions (flowdependent) and spawner population size. A reliable population estimate developed concurrentlywith redd surveys should allow this distinction. An intensive spawner escapement survey alsoprovides additional baseline information on egg retention (pre-spawning mortality), age and sexcomposition, and behavior relative to habitat conditions and population size.


    Salmon spawner surveys were first conducted in the mainstem Sacramento River in 1937 toevaluate the potential effect of Shasta Dam on chinook salmon. From 1937 through 1942, salmonwere counted as they passed through a fish ladder at Anderson-Cottonwood Irrigation Districts(ACID) dam (river mile ), near Redding (Fry 1961) (Needham et. al.1943). The counts weremade to determine the number of fish that would be blocked by Shasta Dam. The counts weremade by the Division of Fish and Game (became the Department of Fish and Game in 1952) in1937, the U. S. Bureau of Reclamation from 1938 through 1941, and the FWS in 1942. ACIDDam is a low, flash board dam that is typically installed in April and is maintained until October orearly November. During both installation and dismantling, fish could jump over the flash boardsand avoid being counted. Excessively high spring flows sometimes delayed installation of theflash boards and prevented counts.

    From 1943 through 1945, salmon spawner counts on the mainstem were made at Balls Ferry(river mile 276). A rack was built for counting and trapping salmon. It was also intended to forcepart of the population to spawn downstream to reduce spawning density between Balls Ferry and

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    the recently constructed Keswick Dam (river mile 302). Many fish passed this rack uncountedduring periods of high flows and by moving through holes underneath the rack.

    Fry (1961) concluded that the 1940's spawner escapement estimates for the mainstem wereprobably much lower than the actual population. This was due to both the tendency to overratethe ability to observe, thus count fish moving through the weir, even when visibility seemedexcellent, and to underestimate how many salmon went through small holes in the counting weir. From 1946 through 1952 a variety of methods were used by both the DFG and FWS to estimatesalmon spawning escapement to the mainstem. Both ground and aerial surveys were made tocount carcasses and redds. The estimates were substantially based upon these data andprofessional judgement using the experience of individuals associated with the program. Theseestimates were never tested against other methods or counts.

    DFG also used a tag-and-recovery method from the 1950 through 1955 to estimate populations inthe mainstem Sacramento River (Fry 1961). Live fish were captured in fyke traps locateddownstream of the spawning grounds, at Fremont Weir (river mile 84), then tagged and released. The tags were later recovered from the carcasses during spawning area surveys, upstream of rivermile 200. This method was satisfactory on the American and Stanislaus rivers, but proved muchless satisfactory on the mainstem Sacramento River (Fry 1961). He gave the following reasonsfor this method being unsatisfactory: (I) the difficulty of recovering adequate numbers ofspawned-out carcasses; (ii) the trapping site was too far below the spawning area; and (iii) thetrap selected for smaller fish.

    From 1956 through 1968, spawner estimates were made by experienced DFG biologists usingcarcass counts(no tag-recapture estimates were made), aerial redd counts, and comparisons withprevious years observations (Dick Hallock, pers. comm). Turbidity, flow, and number of surveytrips were integrated into the estimate. Using the estimate and the carcass counts, carcassrecovery was estimated to range from 0.7 to 4.0%.

    Beginning in 1969, estimates were based on fish counts made at the fish ladders on Red BluffDiversion Dam (RBDD) at river mile 243 (Menchen 1970). The counts were adjusted for periodswhen no counts were made, including when the dam was open due to normal operation or duringfloods, and during night hours when no counts were made. The estimated number of fish caughtby anglers was subtracted from the number passing over RBDD to calculate spawner escapement. Aerial redd counts were used to determine the distribution of spawning upstream and downstreamof RBDD. These results were used to expand RBDD counts and calculate a total estimate for theentire mainstem.

    Since 1986, the gates at RBDD have been raised in the fall and lowered during the followingspring to improve fish passage. Since 1994, the gates are normally open between September 15thand May 15th. Direct (fishway) counts cannot be made when the gates are raised. Salmonspawner estimates are now computed by dividing the number of fish counted in the fishway by theestimated portion of the total run represented in the counting period. The estimated portion wasbased on historical data when counts were made year around.

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    The 1995 escapement survey represents the first attempt since 1968 to estimate salmon spawnerescapement in the mainstem Sacramento River based on the ground surveys. It also representsthe first attempt ever in the mainstem to use carcasses and a tag-recapture model to estimatespawner escapement.

    When monitoring stocks over a long period, such as the Central Valley salmon escapementsurveys, the sampling design should assure the data be collected in a consistent manner andrepresent the population as a whole (Ney 1993). Inconsistencies in methods before 1968 wereprimarily due to changes in funding that often reduced or eliminated sampling effort, thus the dataused to make estimates. Also, population estimates were often based on counts made upstream ofwhere varying portions of the salmon population would spawn - ACID Dam, Balls Ferry Racks,and RBDD. This limited the ability to consistently estimate the entire spawning population unlessspawning distribution was also measured. Another limitation was the unknown number of fishthat could migrate uncounted above the counting sites. This prompted Fry and Petrovich (1970)to conclude: Until we can determine the magnitude of salmon movement through the gates at theRed Bluff Dam the counts there cannot be regarded as more than an index.


    # To estimate the 1995, in-river, fall-run chinook salmon spawning population for themainstem Sacramento River.

    # To augment redd surveys to provide baseline information on spawning distribution,spawning habitat availability, instream flow requirements, and the status of chinooksalmon in the mainstem Sacramento River.


    A carcass tag-and-recapture study was conducted in the mainstem Sacramento River during fall-winter 1995 to estimate fall-run chinook salmon spawner escapement. The study sectionextended 25.5 miles from ACID Dam downstream (river mile 298.5) to Cottonwood Creek (rivermile 273) (Figure 1). Carcasses were tagged and released into running water for later recapture,unlike the earlier tag-and-recovery study when live fish were tagged and released at Fremont weir. Carcass tag-and-recapture studies along with use of the Schaefer or Jolly-Seber models have beenregularly used to estimate escapements in other Central Valley tributary str


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